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- PDB-1imd: STRUCTURAL STUDIES OF METAL BINDING BY INOSITOL MONOPHOSPHATASE: ... -

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Basic information

Entry
Database: PDB / ID: 1imd
TitleSTRUCTURAL STUDIES OF METAL BINDING BY INOSITOL MONOPHOSPHATASE: EVIDENCE FOR TWO-METAL ION CATALYSIS
ComponentsINOSITOL MONOPHOSPHATASEInositol-phosphate phosphatase
KeywordsHYDROLASE
Function / homology
Function and homology information


D-galactose 1-phosphate phosphatase / inositol monophosphate phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / lithium ion binding / inositol biosynthetic process / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / inositol metabolic process ...D-galactose 1-phosphate phosphatase / inositol monophosphate phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / lithium ion binding / inositol biosynthetic process / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / inositol metabolic process / phosphatidylinositol biosynthetic process / phosphate-containing compound metabolic process / phosphatidylinositol phosphate biosynthetic process / manganese ion binding / magnesium ion binding / signal transduction / protein homodimerization activity / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Inositol monophosphatase, lithium-sensitive / Inositol monophosphatase / Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 ...Inositol monophosphatase, lithium-sensitive / Inositol monophosphatase / Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Inositol monophosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsBone, R.
Citation
Journal: Biochemistry / Year: 1994
Title: Structural studies of metal binding by inositol monophosphatase: evidence for two-metal ion catalysis.
Authors: Bone, R. / Frank, L. / Springer, J.P. / Atack, J.R.
#1: Journal: Biochem.J. / Year: 1992
Title: Cdna Cloning of Human and Rat Brain Myo-Inositol Monophosphatase. Expression and Characterization of the Human Recombinant Enzyme
Authors: Mcallister, G. / Whiting, P. / Hammond, E.A. / Knowles, M.R. / Atack, J.R. / Bailey, F.J. / Maigetter, R. / Ragan, C.I.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Structure of Inositol Monophosphatase, the Putative Target of Lithium Therapy
Authors: Bone, R. / Springer, J.P. / Atack, J.R.
History
DepositionFeb 8, 1994Processing site: BNL
Revision 1.0Feb 27, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INOSITOL MONOPHOSPHATASE
B: INOSITOL MONOPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8498
Polymers60,4402
Non-polymers4106
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-64 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.850, 85.850, 153.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: TYR A 62 - PRO A 63 OMEGA = 211.14 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO A 186
3: PHE B 102 - PRO B 103 OMEGA = 211.75 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: CIS PROLINE - PRO B 186

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Components

#1: Protein INOSITOL MONOPHOSPHATASE / Inositol-phosphate phosphatase


Mass: 30219.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDNA / Organ: BRAIN / References: UniProt: P29218, inositol-phosphate phosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %PEG80001reservoir
25 mMglutathione1reservoir
35 mM1reservoirMnCl2
43 mM1reservoirNaN3
550 mM4-morpholinepropanesulfonic acid1reservoir
61 mMEGTA1drop
72 mMo-phenanthroline1drop
820 mMTris1drop
910-15 mg/mLphosphate1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / % possible obs: 95 % / Rmerge(I) obs: 0.083

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→8 Å / Rfactor Rwork: 0.188 / Rfactor obs: 0.188 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4093 0 14 50 4157
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.25
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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